Tripeptides from synthetic amino acids block the Tat-TAR association and slow down HIV spread in cell cultures

Target-Directed Approaches for Screening Small Molecules against RNA Targets

RNA molecules have a variety of cellular functions that can drive disease pathologies. They are without a doubt one of the most intriguing yet controversial small-molecule drug targets. The ability to widely target RNA with small molecules could be revolutionary, once the right tools, assays, and targets are selected, thereby defining which biomolecules are targetable and what constitutes drug-like small molecules. Indeed, approaches developed over the past 5-10 years have changed the face of small molecule-RNA targeting by addressing historic concerns regarding affinity, selectivity, and structural dynamics. Presently, selective RNA-protein complex stabilizing drugs such as branaplam and risdiplam are in clinical trials for the modulation of SMN2 splicing, compounds identified from phenotypic screens with serendipitous outcomes. Fully developing RNA as a druggable target will require a target engagement-driven approach, and evolving chemical collections will be important for the industrial development of this class of target. In this review we discuss target-directed approaches that can be used to identify RNA-binding compounds and the chemical knowledge we have today of small-molecule RNA binders.

Fluorescent indicator displacement assays to identify and characterize small molecule interactions with RNA

Fluorescent indicator displacement (FID) assays are an advantageous approach to convert receptors into optical sensors that can detect binding of various ligands. In particular, the identification of ligands that bind to RNA receptors has become of increasing interest as the roles of RNA in cellular processes and disease pathogenesis continue to be discovered. Small molecules have been validated as tools to elucidate unknown RNA functions, underscoring the critical need to rapidly identify and quantitatively characterize RNA:small molecule interactions for the development of chemical probes. The successful application of FID assays to evaluate interactions between diverse RNA receptors and small molecules has been facilitated by the characterization of distinct fluorescent indicators that reversibly bind RNA and modulate the fluorescence signal. The utility of RNA-based FID assays to both academia and industry has been demonstrated through numerous uses in high-throughput screening efforts, structure-activity relationship studies, and in vitro target engagement studies. Furthermore, the development, optimization, and validation of a variety of RNA-based FID assays has led to general guidelines that can be utilized for facile implementation of the method with new or underexplored RNA receptors. Altogether, the use of RNA-based FID assays as a general analysis tool has provided valuable insights into small molecule affinity and selectivity, furthering the fundamental understanding of RNA:small molecule recognition. In this review, we will summarize efforts to employ FID assays using RNA receptors and describe the significant contributions of the method towards the development of chemical probes to reveal unknown RNA functions.

Fluorescent peptide displacement as a general assay for screening small molecule libraries against RNA

A prominent hurdle in developing small molecule probes against RNA is the relative scarcity of general screening methods. In this study, we demonstrate the application of a fluorescent peptide displacement assay to screen small molecule probes against four different RNA targets. The designed experimental protocol combined with statistical analysis provides a fast and convenient method to simultaneously evaluate small molecule libraries against different RNA targets and classify them based on affinity and selectivity patterns.

Recognition of HIV-TAR RNA using neomycin-benzimidazole conjugates

Synthesis of a novel class of compounds and their biophysical studies with TAR-RNA are presented. The synthesis of these compounds was achieved by conjugating neomycin, an aminoglycoside, with benzimidazoles modeled from a B-DNA minor groove binder, Hoechst 33258. The neomycin-benzimidazole conjugates have varying linkers that connect the benzimidazole and neomycin units. The linkers of varying length (5-23 atoms) in these conjugates contain one to three triazole units. The UV thermal denaturation experiments showed that the conjugates resulted in greater stabilization of the TAR-RNA than either neomycin or benzimidazole used in the synthesis of conjugates. These results were corroborated by the FID displacement and tat-TAR inhibition assays. The binding of ligands to the TAR-RNA is affected by the length and composition of the linker. Our results show that increasing the number of triazole groups and the linker length in these compounds have diminishing effect on the binding to TAR-RNA. Compounds that have shorter linker length and fewer triazole units in the linker displayed increased affinity towards the TAR RNA.

A small-molecule probe induces a conformation in HIV TAR RNA capable of binding drug-like fragments

The HIV-1 transactivation response (TAR) element-Tat interaction is a potentially valuable target for treating HIV infection, but efforts to develop TAR-binding antiviral drugs have not yet yielded a successful candidate for clinical development. In this work, we describe a novel approach toward screening fragments against RNA that uses a chemical probe to target the Tat-binding region of TAR. This probe fulfills two critical roles in the screen: by locking the RNA into a conformation capable of binding other fragments, it simultaneously allows the identification of proximal binding fragments by ligand-based NMR. Using this approach, we have discovered six novel TAR-binding fragments, three of which were docked relative to the probe-RNA structure using experimental NMR restraints. The consistent orientations of functional groups in our data-driven docked structures and common electrostatic properties across all fragment leads reveal a surprising level of selectivity by our fragment-sized screening hits. These models further suggest linking strategies for the development of higher-affinity lead compounds for the inhibition of the TAR-Tat interaction.

Strategies for recognition of stem-loop RNA structures by synthetic ligands: application to the HIV-1 frameshift stimulatory sequence

Production of the Gag-Pol polyprotein in human immunodeficiency virus (HIV) requires a -1 ribosomal frameshift, which is directed by a highly conserved RNA stem-loop. Building on our discovery of a set of disulfide-containing peptides that bind this RNA, we describe medicinal chemistry efforts designed to begin to understand the structure-activity relationships and RNA sequence-selectivity relationships associated with these compounds. Additionally, we have prepared analogues incorporating an olefin or saturated hydrocarbon bioisostere of the disulfide moiety, as a first step toward enhancing biostability. The olefin-containing compounds exhibit affinity comparable to the lead disulfide and, importantly, have no discernible toxicity when incubated with human fibroblasts at concentrations up to 1 mM.

Multivalent binding oligomers inhibit HIV Tat-TAR interaction critical for viral replication

We describe the development of a new type of scaffold to target RNA structures. Multivalent binding oligomers (MBOs) are molecules in which multiple sidechains extend from a polyamine backbone such that favorable RNA binding occurs. We have used this strategy to develop MBO-based inhibitors to prevent the association of a protein-RNA complex, Tat-TAR, that is essential for HIV replication. In vitro binding assays combined with model cell-based assays demonstrate that the optimal MBOs inhibit Tat-TAR binding at low micromolar concentrations. Antiviral studies are also consistent with the in vitro and cell-based assays. MBOs provide a framework for the development of future RNA-targeting molecules.

Structures of HIV TAR RNA-ligand complexes reveal higher binding stoichiometries

Target TAR by NMR: Tripeptides containing arginines as terminal residues and non-natural amino acids as central residues are good leads for drug design to target the HIV trans-activation response element (TAR). The structural characterization of the RNA-ligand complex by NMR spectroscopy reveals two specific binding sites that are located at bulge residue U23 and around the pyrimidine-stretch U40-C41-U42 directly adjacent to the bulge.